# periodic boundary conditions along all three dimensions boundary p p p # Set neighbor skin variable neigh_skin equal 2.0*${_u_distance} variable neigh_skin equal 2.0*1 neighbor ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.147199973464012*${_u_distance} variable latticeconst_converted equal 3.147199973464012*1 lattice bcc ${latticeconst_converted} lattice bcc 3.14719997346401 Lattice spacing in x,y,z = 3.1472 3.1472 3.1472 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (31.472 31.472 31.472) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (31.472 31.472 31.472) create_atoms CPU = 0.000 seconds variable mass_converted equal 95.94*${_u_mass} variable mass_converted equal 95.94*1 kim interactions Mo #=== BEGIN kim interactions ================================== pair_style kim EAM_MagneticCubic_DerletNguyenDudarev_2007_Mo__MO_424746498193_002 WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) pair_coeff * * Mo #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 95.94 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 31172.5992775416 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31172.5992775416/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31172.5992775416/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 31172.5992775416/(1*1*${_u_distance}) variable V0_metal equal 31172.5992775416/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 31172.5992775416*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 31172.5992775416 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*1 variable Tdamp_converted equal 0.01*${_u_time} variable Tdamp_converted equal 0.01*1 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*1 variable Pdamp_converted equal 0.1*${_u_time} variable Pdamp_converted equal 0.1*1 # create initial velocities consistent with the chosen temperature velocity all create ${temp_converted} 17 mom yes rot yes velocity all create 253.15 17 mom yes rot yes # set NPT ensemble for all atoms fix ensemble all npt temp ${temp_converted} ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_u_energy} variable etotal_metal equal etotal/1 variable pe_metal equal pe/${_u_energy} variable pe_metal equal pe/1 variable T_metal equal temp/${_u_temperature} variable T_metal equal temp/1 variable V_metal equal vol/(${_u_distance}*${_u_distance}*${_u_distance}) variable V_metal equal vol/(1*${_u_distance}*${_u_distance}) variable V_metal equal vol/(1*1*${_u_distance}) variable V_metal equal vol/(1*1*1) variable P_metal equal press/${_u_pressure} variable P_metal equal press/1 fix avgmyTemp all ave/time 5 20 100 v_T_metal ave running start 1000 fix avgmyPress all ave/time 5 20 100 v_P_metal ave running start 1000 fix avgmyVol all ave/time 5 20 100 v_V_metal ave running start 1000 # extract fix quantities into variables so they can be used in if-else logic later. variable T equal f_avgmyTemp variable P equal f_avgmyPress variable V equal f_avgmyVol # set error bounds for temperature and pressure in original metal units (K and bar) variable T_low equal "253.15 - 1.0" variable T_up equal "253.15 + 1.0" variable P_low equal "0.0 - 5.0" variable P_up equal "0.0 + 5.0" # print to logfile every 1000 timesteps thermo_style custom step etotal v_etotal_metal pe v_pe_metal temp v_T_metal vol v_V_metal press v_P_metal thermo 1000 # Run a simulation for at most 2000*1000 timesteps. At each 1000th time step, check # whether the temperature and pressure have converged. If yes, break. label top variable a loop 2000 run 1000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM Project: doi:10.1007/s11837-011-0102-6 @Article{tadmor:elliott:2011, author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker}, title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels}, journal = {{JOM}}, year = 2011, volume = 63, number = 17, pages = {17}, doi = {10.1007/s11837-011-0102-6} } - OpenKIM potential: https://openkim.org/cite/MO_424746498193_002#item-citation CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -13574.588 -13574.588 -13640 -13640 253.15 253.15 31172.599 31172.599 2241.2997 2241.2997 1000 -13515.213 -13515.213 -13578.546 -13578.546 245.10546 245.10546 31176.042 31176.042 -747.83767 -747.83767 Loop time of 2.37955 on 1 procs for 1000 steps with 2000 atoms Performance: 36.309 ns/day, 0.661 hours/ns, 420.247 timesteps/s, 840.494 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.303 | 2.303 | 2.303 | 0.0 | 96.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011108 | 0.011108 | 0.011108 | 0.0 | 0.47 Output | 9.2523e-05 | 9.2523e-05 | 9.2523e-05 | 0.0 | 0.00 Modify | 0.060449 | 0.060449 | 0.060449 | 0.0 | 2.54 Other | | 0.004876 | | | 0.20 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2941 ave 2941 max 2941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 116000 ave 116000 max 116000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116000 Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 252.67658072811, Press = 70.3287196007318 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.702 | 3.702 | 3.702 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -13515.213 -13515.213 -13578.546 -13578.546 245.10546 245.10546 31176.042 31176.042 -747.83767 -747.83767 2000 -13511.59 -13511.59 -13576.99 -13576.99 253.10777 253.10777 31186.27 31186.27 -1762.4948 -1762.4948 Loop time of 3.17372 on 1 procs for 1000 steps with 2000 atoms Performance: 27.224 ns/day, 0.882 hours/ns, 315.087 timesteps/s, 630.174 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0936 | 3.0936 | 3.0936 | 0.0 | 97.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01159 | 0.01159 | 0.01159 | 0.0 | 0.37 Output | 3.0727e-05 | 3.0727e-05 | 3.0727e-05 | 0.0 | 0.00 Modify | 0.063309 | 0.063309 | 0.063309 | 0.0 | 1.99 Other | | 0.005187 | | | 0.16 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3096 ave 3096 max 3096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118238 ave 118238 max 118238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118238 Ave neighs/atom = 59.119 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 253.413427986456, Press = 5.52814137501287 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -13511.59 -13511.59 -13576.99 -13576.99 253.10777 253.10777 31186.27 31186.27 -1762.4948 -1762.4948 3000 -13511.439 -13511.439 -13577.396 -13577.396 255.26056 255.26056 31149.432 31149.432 1941.9769 1941.9769 Loop time of 3.19049 on 1 procs for 1000 steps with 2000 atoms Performance: 27.080 ns/day, 0.886 hours/ns, 313.431 timesteps/s, 626.863 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1115 | 3.1115 | 3.1115 | 0.0 | 97.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011294 | 0.011294 | 0.011294 | 0.0 | 0.35 Output | 3.1609e-05 | 3.1609e-05 | 3.1609e-05 | 0.0 | 0.00 Modify | 0.062616 | 0.062616 | 0.062616 | 0.0 | 1.96 Other | | 0.00507 | | | 0.16 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3037 ave 3037 max 3037 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118266 ave 118266 max 118266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118266 Ave neighs/atom = 59.133 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 253.223554260891, Press = 7.51243638346283 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.702 | 3.702 | 3.702 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -13511.439 -13511.439 -13577.396 -13577.396 255.26056 255.26056 31149.432 31149.432 1941.9769 1941.9769 4000 -13509.041 -13509.041 -13575.222 -13575.222 256.12756 256.12756 31147.637 31147.637 1751.1765 1751.1765 Loop time of 3.19064 on 1 procs for 1000 steps with 2000 atoms Performance: 27.079 ns/day, 0.886 hours/ns, 313.417 timesteps/s, 626.834 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1112 | 3.1112 | 3.1112 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011503 | 0.011503 | 0.011503 | 0.0 | 0.36 Output | 4.8851e-05 | 4.8851e-05 | 4.8851e-05 | 0.0 | 0.00 Modify | 0.062796 | 0.062796 | 0.062796 | 0.0 | 1.97 Other | | 0.005088 | | | 0.16 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3074 ave 3074 max 3074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118376 ave 118376 max 118376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118376 Ave neighs/atom = 59.188 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" jump SELF break # Write final averaged volume to file if temperature and volume have converged; otherwise wirte a # flag to indicate non-convergence. variable myStep equal step if "${myStep} < 2000000" then "print '${V}' file output/vol_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 31167.2437391653 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0